Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,642,401 C→T 8.8% T1082T (ACG→ACA)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,642,4010CT 8.8% 118.2 / 2.7 45T1082T (ACG→ACA) yfhMbacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (17/24);  new base T (2/2);  total (19/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.94e-01

CGTTTGTGCCGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGCCAC  >  CP009273/2642254‑2642549
                                                                                                                                                   |                                                                                                                                                    
cGTTTGTGCCGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCg                                                                                                                                                     <  2:110578/149‑1 (MQ=255)
  tttGTGCCGGGAACGCCGGACGGATGCCGTTTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTACCCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCgta                                                                                                                                                   <  2:167779/149‑1 (MQ=255)
        ccgcaaaCGCAAGACGGACGCCGATTTTCCACTTCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATACACAGcaga                                                                                                                                                   >  1:332345/6‑140 (MQ=255)
        ccGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGc                                                                                                                                             >  2:306907/1‑149 (MQ=255)
        ccGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCAGGCCCCGGGATAAACAGCgca                                                                                                                                                   >  1:228432/1‑141 (MQ=255)
        ccGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCGAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAAAGCGCGCACCGGGAAAAACAACgaa                                                                                                                                                   >  1:110748/1‑141 (MQ=255)
              aCGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGAGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCCCACCt                                                                                                                                       >  2:235984/1‑149 (MQ=255)
               cGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGca                                                                                                                                            >  1:273645/1‑143 (MQ=255)
                  cggacggaCGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGgcg                                                                                                                                   <  2:542695/149‑1 (MQ=255)
                                ttttCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCt                                                                                                                     >  2:139898/1‑149 (MQ=255)
                                     cACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCggg                                                                                                                <  2:422058/149‑1 (MQ=255)
                                      aCTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGt                                                                                                               <  2:219931/149‑1 (MQ=255)
                                        tGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGATCAGTAGAGTTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGa                                                                                                             <  2:463860/149‑1 (MQ=255)
                                              tGCCGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCt                                                                                                       <  2:287056/149‑1 (MQ=255)
                                               gCTGATCGGCCACGGTTCCACCCGGTAACGGTAACCCGCGAATGGTGGCCTGCATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGaa                                                                                                            <  1:512679/143‑1 (MQ=255)
                                                 tGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGAc                                                                                                    >  2:126801/1‑149 (MQ=255)
                                                 tGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGAc                                                                                                    >  2:126136/1‑149 (MQ=255)
                                                      ggCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGGGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGAGAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCtta                                                                                                     <  1:179874/143‑3 (MQ=255)
                                                        cAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTGCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCa                                                                                             <  2:256720/149‑1 (MQ=255)
                                                         aaCGGTTTCGCCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTaaa                                                                                            <  2:635079/149‑1 (MQ=255)
                                                             gTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCaa                                                                                        >  2:483380/1‑149 (MQ=255)
                                                             gTTTCACCCGGTAACGCTAACCCGCTAATGGGGGCCAGAACTTCTCCACCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCaa                                                                                        <  2:119501/149‑1 (MQ=255)
                                                                       gTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCg                                                                              <  2:339719/149‑1 (MQ=255)
                                                                       gTAACGCTAACCCGCTAAGGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCg                                                                              <  2:344689/149‑1 (MQ=255)
                                                                            gCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCCCCAGGAAAAAAACCGTAGCACGCACAGCCAGCGCTAAGTCAGCGGCTGGTACGGAATCGCGGACCAGTTCAAGCAAACCACCGGc                                                                               >  1:418767/1‑143 (MQ=255)
                                                                                       aaTGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCaa                                                                    <  1:82859/143‑1 (MQ=255)
                                                                                       aaTGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCa                                                              <  2:372575/149‑1 (MQ=255)
                                                                                              gCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTCCGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAGCCGAACCACTAGCGACCAGGGCAACGTTCAGTTTTTg                                                       >  2:174788/1‑149 (MQ=255)
                                                                                                 tGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCgg                                                    >  2:257111/1‑149 (MQ=255)
                                                                                                   aaTTTCTCCATCGCCATACCCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGtt                                                  <  2:48453/149‑1 (MQ=255)
                                                                                                      ttCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCACAGTTCAGTTTTTGCg                                                     >  1:447725/1‑143 (MQ=255)
                                                                                                           cATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAAAGTTCGGTTTTTGCGGGTTa                                                >  1:170338/1‑143 (MQ=255)
                                                                                                            aTCGCCATAACCCGGCAATGCTCGCACCAGGATAAACAGCGTAGTACACACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTGAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         >  2:357494/1‑149 (MQ=255)
                                                                                                             ccctcATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATc                                              <  1:517862/139‑1 (MQ=255)
                                                                                                                  aTAACCCGGCAATGCTCGCACCGGGATAAACCGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCTATTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAg                                   <  2:427106/149‑1 (MQ=255)
                                                                                                                  aTAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         <  1:113205/143‑1 (MQ=255)
                                                                                                                  aTAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         <  1:113804/143‑1 (MQ=255)
                                                                                                                  aTAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         <  1:140383/143‑1 (MQ=255)
                                                                                                                  aTAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTATGCGGATTATCGGTAAGATTAg                                   >  2:181659/1‑149 (MQ=255)
                                                                                                                          gCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGGTATcc                           >  2:510988/1‑149 (MQ=255)
                                                                                                                           cAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATGGCTGACCAGTTCAAGCAAACCCCTGGCGGTCAGGGCACCGGTCAGTTTTTGCGGTTTATCGGTGAGGTTAGTGa                                >  1:452291/1‑143 (MQ=255)
                                                                                                                              tGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGatat                             <  1:529345/143‑1 (MQ=255)
                                                                                                                               gCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATc                            <  1:130671/143‑1 (MQ=255)
                                                                                                                                        gggATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTAACGCTGCGCTGTAAGATTAGTGATATCCAGCGTCAGACGCGa             <  2:311128/149‑1 (MQ=255)
                                                                                                                                            tAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGAcgc               <  1:499065/143‑1 (MQ=255)
                                                                                                                                                  gCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGGCTAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGccg   >  2:283147/1‑148 (MQ=255)
                                                                                                                                                   cGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGCCAc  >  2:615158/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                    
CGTTTGTGCCGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGCCAC  >  CP009273/2642254‑2642549

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑